When I manually synchronized my entire user profile from my MacBook Pro to my MacBook air, the next Sync on the new MacBook Air behaved normally, and didn't remove anything.

You might be able to get by by just copying your ~/Library/MobileDevice , ~/Library/Application Support/MobileSync , and your ~/Music/iTunes directories to your user account on your new Mac, but you'd have to do some experimentation to find the required set of directories to keep in sync between the 2 Macs.

I don't do this with iTunes, but I have a method for syncing apps between machines that works very well.

First, install Dropbox or an equivalent file-syncing solution.

Then, create a directory for the configuration and library files of the application (I use ~/Dropbox/config/appname/). Move the relevant config directories in there. Usually, this would be ~/Library/Application Support/Appname/ and possibly some .plist files in ~/Library/Preferences/. Then you also need to move the actual library into dropbox.

Then, create symbolic links to those new locations from the places where the application expects them. Since iTunes can be configured to place its library (the actual music files) in any folder, you don't need to accomplish this by means of a symlink. The command for creating symlinks are as follows and must be executed in a terminal:

ln -s newlocation expectedlocation

E.g.:

ln -s ~/Dropbox/Config/iTunes ~/Library/Application\ Support/iTunes

If you do this on both machines (on the second - delete all the config files, you should have copied the library you wish to replicate into dropbox) and you don't open the software at the same time on both machines, you should be synced.